So I finished the current game (all bosses with both characters) and I have a couple of suggestions-
I'm not sure I like the multiple health bars. They make it difficult to tell how close I am to killing an enemy. It's a cool visual so I think it can be made to work, but it might be worth adding an option for a % health indicator or a single health bar.
Have you considered using abbreviations for large numbers (ex. 100k instead of 100000)? It's not a problem now, but if the numbers grow exponentially as the progression continues it could become one.
I know this comment is getting long, but one more suggestion I have is having the character skill screen and character select default to the character last played, instead of defaulting to the first character. When I played the second character it got a bit annoying having to manually change to him every time I finished a run.
I hope the feedback is helpful, feel free to ignore if you disagree, you are clearly better at this than me. Regardless, the game is awesome and I'm definitely looking forward to playing the final product.